1 / 9

Making a Network in Cytoscape

Making a Network in Cytoscape. Step 1: Research your network. http://oceanlink.island.net/oinfo/foodweb/foodweb.html. Understanding The Food Web. One type of interaction in this food web: organisms eating other organisms This web page tells me that: Salmon eats herring

vielka-schultz
Télécharger la présentation

Making a Network in Cytoscape

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Making a Network in Cytoscape

  2. Step 1: Research your network http://oceanlink.island.net/oinfo/foodweb/foodweb.html

  3. Understanding The Food Web • Onetype of interaction in this food web: organisms eating other organisms • This web page tells me that: • Salmon eats herring • Salmon is eaten by seals, killer whales, sea birds, scavengers, and decomposers • The energy flow in a food web moves from organisms which are eaten towards organisms which eat them.

  4. Column 3 = organism Column 1 = organism Column 2 = interaction (is eaten by) Step 1: Create a SIF (Simple Interaction Format) File Create a 3 column file in Excel:

  5. Save your SIF file • File Name: Write in .sif at the end of the file name, and include the entire file name in quotation marks: For example: “myfoodweb.sif” • Save as type: Text (Tab Delimited) File name Save as type

  6. Open up this page: Then click on the “Click Here to Start” Link. Step 2: Open a Blank Cytoscape http://halo.systemsbiology.net/cytoscape/blank

  7. File Load Interaction… your SIF file Step 3: load SIF file into Cytoscape

  8. Cytoscape createsa network: • This type of layout is “Organic” • See “Layout” menu to explore different layouts (choose a layout, then press Control-L). • See “Visualization” menu to explore visual aspects of network.

  9. More info, bigger network

More Related